Sequence‐dependent clustering properties of nucleotides fragments in an ionic solution

Abstract

AbstractThe chemical nature of the DNA bases is an important factor in sequence‐mediated association of DNA molecules. Nucleotides are the fundamental DNA elements and the base identity impacts the molecular properties of nucleotide fragments. It is interesting to study the fundamental nature of nucleotides in DNA, on the basis of base‐specific interactions, association, and modes of standard atomic or molecular interactions. With all‐atom molecular dynamics simulations of model dinucleotide and tetranucleotide systems having single‐stranded dinucleotide or tetranucleotide fragments of varying sequences, we show how the base identity and interactions between the different bases as well as water may affect the clustering properties of nucleotides fragments in an ionic solution. Sequence‐dependent differential interactions between the nucleotide fragments, ionic concentration, and elevated temperature are found to influence the clustering properties and dynamics of association. Well‐known epigenetic modification of DNA, that is, cytosine methylation also promotes dinucleotide clustering in solution. These observations point to one possible chemical nature of the DNA bases, as well as the importance of the base pairing, base stacking, and ionic interactions in DNA structure formation, and DNA sequence‐mediated association. Sequence‐ and the ionic environment‐mediated self‐association properties of the dinucleotides indicate its great potential to develop biological nanomaterials for desired applications.